Research workbench
Crystal structure of dihydrodipicolinate synthase from bacillus anthracis in complex with its substrate, pyruvate
Analyse Crystal structure of dihydrodipicolinate synthase from bacillus anthracis in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HIJ
- Type
- protein
- Length
- 1,168 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrodipicolinate synthase
- UniProt
- Q81WN7
- Ligands
- NA
- Pockets
- 11 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Dihydrodipicolinate synthase | protein | 292 | 50% helix, 13% strand | Q81WN7 |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 511 | 0.73 | 0.82 | 52 | empty |
| 2 | 462 | 0.71 | 0.82 | 39 | empty |
| 3 | 227 | 0.54 | 0.77 | 35 | empty |
| 4 | 203 | 0.53 | 0.78 | 31 | empty |
| 5 | 215 | 0.52 | 0.77 | 37 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1436 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1416 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 967 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 963 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nonstandard).
Compared structures
- 3HIJ · Crystal structure of dihydrodipicolinate synthase from Bacillus anthracis in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q81WN7
- Elsewhere: RCSB PDB 3HIJ · PDBe 3HIJ · UniProt Q81WN7
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